error in utils compiation
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Hoover, David (NIH/CIT) [E]
Nov 12, 2024, 7:24:29 PM11/12/24
to genome...@soe.ucsc.edu
Hi,
I tried compiling the utils for v473 and got this error when trying `make libs`:
> psGfx.c: In function ‘psOpen’:
> psGfx.c:131:7: error: ‘encodeFont’ undeclared (first use in this function)
> fputs(encodeFont, ps->f);
> ^~~~~~~~~~
> psGfx.c:131:7: note: each undeclared identifier is reported only once for each function it appears in
> make[1]: *** [../inc/common.mk:388: psGfx.o] Error 1
It then went on to fail the libs compilation:
> cc: error: ../../lib/x86_64/jkweb.a: No such file or directory
> cc: error: ../../htslib/libhts.a: No such file or directory
> cc: error: ../../htslib/libhts.a: No such file or directory
> make[1]: *** [makefile:12: affyPairsToSample] Error 1
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov
I tried compiling the utils for v473 and got this error when trying `make libs`:
> psGfx.c: In function ‘psOpen’:
> psGfx.c:131:7: error: ‘encodeFont’ undeclared (first use in this function)
> fputs(encodeFont, ps->f);
> ^~~~~~~~~~
> psGfx.c:131:7: note: each undeclared identifier is reported only once for each function it appears in
> make[1]: *** [../inc/common.mk:388: psGfx.o] Error 1
It then went on to fail the libs compilation:
> cc: error: ../../lib/x86_64/jkweb.a: No such file or directory
> cc: error: ../../htslib/libhts.a: No such file or directory
> cc: error: ../../htslib/libhts.a: No such file or directory
> make[1]: *** [makefile:12: affyPairsToSample] Error 1
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov
Hoover, David (NIH/CIT) [E]
Nov 12, 2024, 7:24:32 PM11/12/24
to genome...@soe.ucsc.edu
Also, iconv.h is missing from src/inc.
Jonathan Casper
Nov 13, 2024, 1:57:57 AM11/13/24
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
Hi David,
Thanks for writing in! Just to check, which source package were you compiling utils from? We did recently add a dependency for psGfx.c: reEncodeFont.c, which is generated by another target in the makefile in kent/src/lib/. I just downloaded the source package to be sure, and it looks like the necessary components are there (the make target for reEncodeFont.c and the corresponding input file reEncodeFont.ps). Were those the only error messages you received, or was there anything else (likely earlier, and maybe in reference to "reEncodeFont.c")? It might also be worth doing a "make clean" before the "make libs", just in case the dependency is somehow being skipped.
A version of reEncodeFont.c was also subsequently checked into our source tree. You can find a copy of the file at https://github.com/ucscGenomeBrowser/kent/blob/master/src/lib/reEncodeFont.c and copy that into place if for some reason your system is having trouble generating it.
As for iconv.h, that should be part of the libc6/glibc system package - it's not a library we authored ourselves. Does your system not have iconv.h under /usr/include/ or a similar path?
Best,
Jonathan Casper
UCSC Genome Browser
Thanks for writing in! Just to check, which source package were you compiling utils from? We did recently add a dependency for psGfx.c: reEncodeFont.c, which is generated by another target in the makefile in kent/src/lib/. I just downloaded the source package to be sure, and it looks like the necessary components are there (the make target for reEncodeFont.c and the corresponding input file reEncodeFont.ps). Were those the only error messages you received, or was there anything else (likely earlier, and maybe in reference to "reEncodeFont.c")? It might also be worth doing a "make clean" before the "make libs", just in case the dependency is somehow being skipped.
A version of reEncodeFont.c was also subsequently checked into our source tree. You can find a copy of the file at https://github.com/ucscGenomeBrowser/kent/blob/master/src/lib/reEncodeFont.c and copy that into place if for some reason your system is having trouble generating it.
As for iconv.h, that should be part of the libc6/glibc system package - it's not a library we authored ourselves. Does your system not have iconv.h under /usr/include/ or a similar path?
Best,
Jonathan Casper
UCSC Genome Browser
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Mark Diekhans
Nov 13, 2024, 2:02:39 PM11/13/24
to Hoover, David (NIH/CIT) [E], genome...@soe.ucsc.edu
iconv.h is provided by the linux libiconv package, which I think is brought
in by install freetype.
encodeFont is in kent/src/lib/reEncodeFont.c
which is generated by the makefile
If something when wrong and it is empty, remove it and recompile
Hoover, David (NIH/CIT) [E]
Nov 13, 2024, 2:02:53 PM11/13/24
to Mark Diekhans, genome...@soe.ucsc.edu
Hi Mark,
Apologies, yes iconv.h is provided by the system packages.
I found if I clone the master branch, rather than v473_branch, the compilation completes normally. I'm not sure what changed between those releases.
David
Apologies, yes iconv.h is provided by the system packages.
I found if I clone the master branch, rather than v473_branch, the compilation completes normally. I'm not sure what changed between those releases.
David
Hoover, David (NIH/CIT) [E]
Nov 13, 2024, 2:03:02 PM11/13/24
to Jonathan Casper, genome...@soe.ucsc.edu
The master branch compiles normally, whereas the v473_branch does not. I'm not sure what changes were made between releases.
David
On 11/13/2024 1:57 AM, Jonathan Casper wrote:
> Hi David,
>
> Thanks for writing in! Just to check, which source package were you compiling utils from? We did recently add a dependency for psGfx.c: reEncodeFont.c, which is generated by another target in the makefile in kent/src/lib/. I just downloaded the source package to be sure, and it looks like the necessary components are there (the make target for reEncodeFont.c and the corresponding input file reEncodeFont.ps). Were those the only error messages you received, or was there anything else (likely earlier, and maybe in reference to "reEncodeFont.c")? It might also be worth doing a "make clean" before the "make libs", just in case the dependency is somehow being skipped.
>
> A version of reEncodeFont.c was also subsequently checked into our source tree. You can find a copy of the file at https://github.com/ucscGenomeBrowser/kent/blob/master/src/lib/reEncodeFont.c <https://github.com/ucscGenomeBrowser/kent/blob/master/src/lib/reEncodeFont.c> and copy that into place if for some reason your system is having trouble generating it.
> To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/7d148275-b611-4e24-8c34-bd984afb5c77%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/7d148275-b611-4e24-8c34-bd984afb5c77%40hpc.nih.gov>.
David
On 11/13/2024 1:57 AM, Jonathan Casper wrote:
> Hi David,
>
> Thanks for writing in! Just to check, which source package were you compiling utils from? We did recently add a dependency for psGfx.c: reEncodeFont.c, which is generated by another target in the makefile in kent/src/lib/. I just downloaded the source package to be sure, and it looks like the necessary components are there (the make target for reEncodeFont.c and the corresponding input file reEncodeFont.ps). Were those the only error messages you received, or was there anything else (likely earlier, and maybe in reference to "reEncodeFont.c")? It might also be worth doing a "make clean" before the "make libs", just in case the dependency is somehow being skipped.
>
>
> As for iconv.h, that should be part of the libc6/glibc system package - it's not a library we authored ourselves. Does your system not have iconv.h under /usr/include/ or a similar path?
>
> Best,
> Jonathan Casper
> UCSC Genome Browser
>
> As for iconv.h, that should be part of the libc6/glibc system package - it's not a library we authored ourselves. Does your system not have iconv.h under /usr/include/ or a similar path?
>
> Best,
> Jonathan Casper
> UCSC Genome Browser
>
> On Tue, Nov 12, 2024 at 4:24 PM 'Hoover, David (NIH/CIT) [E]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu>> wrote:
>
> Also, iconv.h is missing from src/inc.
>
> On 11/12/2024 9:39 AM, Hoover, David (NIH/CIT) [E] wrote:
> > Hi,
> >
> > I tried compiling the utils for v473 and got this error when trying `make libs`:
> >
> >> psGfx.c: In function ‘psOpen’:
> >> psGfx.c:131:7: error: ‘encodeFont’ undeclared (first use in this function)
> >> fputs(encodeFont, ps->f);
> >> ^~~~~~~~~~
> >> psGfx.c:131:7: note: each undeclared identifier is reported only once for each function it appears in
> >> make[1]: *** [../inc/common.mk:388 <http://common.mk:388>: psGfx.o] Error 1
>
> Also, iconv.h is missing from src/inc.
>
> On 11/12/2024 9:39 AM, Hoover, David (NIH/CIT) [E] wrote:
> > Hi,
> >
> > I tried compiling the utils for v473 and got this error when trying `make libs`:
> >
> >> psGfx.c: In function ‘psOpen’:
> >> psGfx.c:131:7: error: ‘encodeFont’ undeclared (first use in this function)
> >> fputs(encodeFont, ps->f);
> >> ^~~~~~~~~~
> >> psGfx.c:131:7: note: each undeclared identifier is reported only once for each function it appears in
> >
> > It then went on to fail the libs compilation:
> >
> >> cc: error: ../../lib/x86_64/jkweb.a: No such file or directory
> >> cc: error: ../../htslib/libhts.a: No such file or directory
> >> cc: error: ../../htslib/libhts.a: No such file or directory
> >> make[1]: *** [makefile:12: affyPairsToSample] Error 1
> >
> > David
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
> Email: hoov...@hpc.nih.gov <mailto:hoov...@hpc.nih.gov>
> > It then went on to fail the libs compilation:
> >
> >> cc: error: ../../lib/x86_64/jkweb.a: No such file or directory
> >> cc: error: ../../htslib/libhts.a: No such file or directory
> >> cc: error: ../../htslib/libhts.a: No such file or directory
> >> make[1]: *** [makefile:12: affyPairsToSample] Error 1
> >
> > David
>
> --
> David Hoover, Ph.D.
> Computational Biologist
> High Performance Computing Services,
> Center for Information Technology,
> National Institutes of Health
> 12 South Dr., Rm 2N207
> Bethesda, MD 20892, USA
> TEL: (+1) 301-435-2986
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu <mailto:genome-mirror%2Bunsu...@soe.ucsc.edu>.
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Mirror-Specific Support" group.
> To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/7d148275-b611-4e24-8c34-bd984afb5c77%40hpc.nih.gov <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/7d148275-b611-4e24-8c34-bd984afb5c77%40hpc.nih.gov>.
Brian Raney
Nov 13, 2024, 2:10:31 PM11/13/24
to Hoover, David (NIH/CIT) [E], Jonathan Casper, genome...@soe.ucsc.edu
What happened was I fixed it after v473 by checking in reEncodeFont.c
instead of requiring it to be built from the reEncodeFont.ps. You
shouldn't see the problem in v474.
Sorry for the trouble. I've learned my lesson. ;-)
brian
On Wed, Nov 13, 2024 at 11:03 AM 'Hoover, David (NIH/CIT) [E]' via
> To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirro...@soe.ucsc.edu.
> To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/8edbdb03-aeb4-4316-9b89-6e25b6093705%40hpc.nih.gov.
instead of requiring it to be built from the reEncodeFont.ps. You
shouldn't see the problem in v474.
Sorry for the trouble. I've learned my lesson. ;-)
brian
On Wed, Nov 13, 2024 at 11:03 AM 'Hoover, David (NIH/CIT) [E]' via
UCSC Genome Browser Mirror-Specific Support
> To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/8edbdb03-aeb4-4316-9b89-6e25b6093705%40hpc.nih.gov.
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